{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "
\n", "\n", "# Python - Neuroimaging Workshop DZNE Magdeburg, September 2019\n", "\n", "Python is on its way to become the most used programming language in neuroscience. It is easy to understand, can be learned rather quickly and has a very strong and helpful community behind it. There exist many amazing neuroimaging software packages, such as Nipype & fmriprep, that facilitate the everyday life of a neuroscientist.\n", "\n", "The goal of this 2-day workshop is to introduce participants to the basics of Python, to give them a short overview about relevant neuroimaging software packages and most of all, to teach them everything they need to know about Nipype. Nipype is an open-source software package, that provides a unified way of interfacing with most of the freely available neuroimaging software packages, such as SPM, FSL, AFNI, FreeSurfer, and ANTs.\n", "\n", "The full content of this course, all notebooks and slides can be found on the github repository [github.com/peerherholz/workshop_magdeburg](https://github.com/peerherholz/workshop_magdeburg).\n", "\n", "### Important 1\n", "If you're running this notebook through a docker container, make sure that you used the `-v` flag to mount a folder on your system inside the container. Like this, you will have access to any output that you create within this container. For more, take a look at the [Docker information](https://github.com/peerherholz/workshop_magdeburg#docker).\n", "\n", "### Important 2\n", "If you used the `-v` flag from above to mount the `output` folder, you can use the following command to save all notebooks (with your changes) and slides in the folder `/output/`. **Just don't forget to run this cell before closing the docker container!**" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# Save the workshop and nipype_tutorial content into your output folder\n", "!cp -R /home/neuro/* /output/" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# Get the saved notebook from the output folder back into this docker image\n", "!cp -R /output/* /home/neuro/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Day 1\n", "\n", "